| 2025 | AAAI | Improving Deep Learning Speed and Performance Through Synaptic Neural Balance. | Antonios Alexos, Ian Domingo, Pierre Baldi |
| 2025 | IJCNN | Optimization of Sparse Phased Arrays Using Deep Learning. | Jackson Earls, Lior Maman, David Lin Yi Lu, Amir Boag, Pierre Baldi |
| 2024 | ICLR | Toward Optimal Policy Population Growth in Two-Player Zero-Sum Games. | Stephen Marcus McAleer, JB Lanier, Kevin A. Wang, Pierre Baldi, Tuomas Sandholm, Roy Fox |
| 2024 | NAACL | Selective Perception: Learning Concise State Descriptions for Language Model Actors. | Kolby Nottingham, Yasaman Razeghi, Kyungmin Kim, JB Lanier, Pierre Baldi, Roy Fox, Sameer Singh |
| 2021 | IJCAI | Deep Bucket Elimination. | Yasaman Razeghi, Kalev Kask, Yadong Lu, Pierre Baldi, Sakshi Agarwal, Rina Dechter |
| 2021 | SCAM | D-REX: Static Detection of Relevant Runtime Exceptions with Location Aware Transformer. | Farima Farmahinifarahani, Yadong Lu, Vaibhav Saini, Pierre Baldi, Cristina V. Lopes |
| 2019 | AAAI | Efficient Neutrino Oscillation Parameter Inference with Gaussian Process. | Lingge Li, Nitish Nayak, Jianming Bian, Pierre Baldi |
| 2019 | ICLR | Solving the Rubik's Cube with Approximate Policy Iteration. | Stephen McAleer, Forest Agostinelli, Alexander Shmakov, Pierre Baldi |
| 2019 | IJCAI | Learning in the Machine: Random Backpropagation and the Deep Learning Channel (Extended Abstract). | Pierre Baldi, Peter J. Sadowski, Zhiqin Lu |
| 2019 | ICSE | Towards automating precision studies of clone detectors. | Vaibhav Saini, Farima Farmahinifarahani, Yadong Lu, Di Yang, Pedro Martins, Hitesh Sajnani, Pierre Baldi, Cristina V. Lopes |
| 2016 | ICMLA | Revealing Fundamental Physics from the Daya Bay Neutrino Experiment Using Deep Neural Networks. | Evan Racah, Seyoon Ko, Peter J. Sadowski, Wahid Bhimji, Craig Tull, Sang-Yun Oh, Pierre Baldi, Prabhat |
| 2011 | CCS | Countering GATTACA: efficient and secure testing of fully-sequenced human genomes. | Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, Gene Tsudik |
| 2010 | IJCNN | A scalable reference-point based algorithm to efficiently search large chemical databases. | Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi |
| 2010 | SEKE | Information-Theoretic Metrics for Project-Level Scattering and Tangling. | Erik Linstead, Lindsey Hughes, Cristina Videira Lopes, Pierre Baldi |
| 2009 | MSR | Mining the coherence of GNOME bug reports with statistical topic models. | Erik Linstead, Pierre Baldi |
| 2009 | MSR | SourcererDB: An aggregated repository of statically analyzed and cross-linked open source Java projects. | Joel Ossher, Sushil Krishna Bajracharya, Erik Linstead, Pierre Baldi, Cristina Videira Lopes |
| 2008 | DCC | Effective Compression of Monotone and Quasi-Monotone Sequences of Integers. | Daniel S. Hirschberg, Pierre Baldi |
| 2008 | ICMLA | An Application of Latent Dirichlet Allocation to Analyzing Software Evolution. | Erik Linstead, Cristina Videira Lopes, Pierre Baldi |
| 2008 | ISMB | BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. | Pierre Baldi, Ryan W. Benz |
| 2008 | OOPSLA | A theory of aspects as latent topics. | Pierre Baldi, Cristina Videira Lopes, Erik Linstead, Sushil Krishna Bajracharya |
| 2007 | ICMLA | Machine Learning Challenges in Chemoinformatics and Drug Screening and Design. | Pierre Baldi |
| 2007 | ISMB | From protein microarrays to diagnostic antigen discovery: a study of the pathogen | Suman Sundaresh, Arlo Z. Randall, Berkay Unal, Jeannine M. Petersen, John T. Belisle, M. Gill Hartley, Melanie Duffield, Richard W. Titball, D. Huw Davies, Philip L. Felgner, Pierre Baldi |
| 2007 | MSR | Mining Eclipse Developer Contributions via Author-Topic Models. | Erik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi |
| 2006 | OOPSLA | Sourcerer: a search engine for open source code supporting structure-based search. | Sushil Krishna Bajracharya, Trung Chi Ngo, Erik Linstead, Yimeng Dou, Paul Rigor, Pierre Baldi, Cristina Videira Lopes |
| 2005 | CVPR | A Principled Approach to Detecting Surprising Events in Video. | Laurent Itti, Pierre Baldi |
| 2005 | ESANN | SVM and pattern-enriched common fate graphs for the game of go. | Liva Ralaivola, Lin Wu, Pierre Baldi |
| 2005 | IJCNN | Exploring chemical space with computers: challenges and opportunities. | Pierre Baldi |
| 2005 | ISMB | Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. | Jianlin Cheng, Pierre Baldi |
| 2005 | ISMB | Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. | Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi |
| 2003 | AI | Machine Learning Methods for Computational Proteomics and Beyond. | Pierre Baldi |
| 2002 | ISMB | Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. | Gianluca Pollastri, Pierre Baldi |
| 2001 | ISMB | Improved prediction of the number of residue contacts in proteins by recurrent neural networks. | Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio |
| 2001 | PSB | Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. | Pierre Baldi, Sren Brunak |
| 2001 | PSB | DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction. | Pierre Baldi, Richard H. Lathrop |
| 2000 | ISMB | Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. | Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Sren Brunak |
| 2000 | ISMB | Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods. | Steven Hampson, Pierre Baldi, Dennis F. Kibler, Suzanne B. Sandmeyer |
| 1998 | ISMB | Computational Applications of DNA Structural Scales. | Pierre Baldi, Sren Brunak, Yves Chauvin, Anders Gorm Pedersen |
| 1996 | ISMB | Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. | Anders Gorm Pedersen, Pierre Baldi, Sren Brunak, Yves Chauvin |
| 1995 | ISMB | Periodic Sequence Patterns in Human Exons. | Pierre Baldi, Sren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh |
| 1995 | ISMB | Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures. | Pierre Baldi, Yves Chauvin |
| 1993 | ESANN | Trajectory learning using hierarchy of oscillatory modules. | Nikzad Benny Toomarian, Pierre Baldi |